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Problems with Fiji after Fiji update

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Avital Steinberg

Problems with Fiji after Fiji update

Hi,
Ever since I updated Fiji, I'm having trouble using it. I uninstalled it
and reinstalled it, and uninstalled Java 7. I'm using mac 10.9.5, with
ImageJ version 2.0.0-rc-43/1.50e, build: 49b667f9aa.

It's running with Java 1.6.0_65 [64 bit].

Various scripts that used to work no longer work with this version of Fiji.
Here's an example:

importClass(Packages.ij.IJ);
importClass(Packages.ij.plugin.frame.RoiManager);
importClass(Packages.ij.io.OpenDialog);
importClass(Packages.ij.io.DirectoryChooser);
importClass(Packages.java.io.File);
importClass(Packages.ij.gui.GenericDialog);
importClass(Packages.ij.util.Tools);
importClass(Packages.ij.plugin.Duplicator);
importClass(Packages.ij.measure.ResultsTable);
importClass(Packages.ij.ImagePlus);
importClass(Packages.ij.process.ImageProcessor);
importClass(Packages.ij.util.ArrayUtil);
importClass(Packages.ij.gui.Overlay);
importClass(Packages.ij.plugin.filter.ParticleAnalyzer);
importClass(Packages.ij.gui.Roi);
importClass(Packages.ij.plugin.RGBStackMerge);
importClass(Packages.ij.process.ImageConverter);
importPackage(java.awt);

dir = "/Users/avitalsteinberg/Javascript /RFP wontRun input/";

dirOutput = dir.substring(0, dir.length - 1)+ "_output/";

if(!File(dirOutput).exists()){
File(dirOutput).mkdir();
}

IJ = IJ();
rm = RoiManager(); // initiating the ROI manager in hidden mode.
if (rm==null)
IJ.error("ROI Manager is not found");
rt = ResultsTable(); // Here, the default is hidden mode.
rt.setValue("yCentroid", 0, 1);
rt.show();

The debugger gives the following error message: (even though the import
exits, highlighted blue)
Can't find method ij.measure.ResultsTable.show()

Any idea what can be done to get Fiji to work well with my computer?

Thanks,
Avital

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ImageJ mailing list: http://imagej.nih.gov/ij/list.html

Brandon Hurr

Re: Problems with Fiji after Fiji update

I don't know for sure, but try running it with Java 8. I have update 51,
60, and 66 and they all work fairly well, especially after the 1.50e
update.

https://www.java.com/en/download/

On Wed, Dec 2, 2015 at 12:07 PM, Avital Steinberg <[hidden email]
> wrote:

> Hi,
> Ever since I updated Fiji, I'm having trouble using it. I uninstalled it
> and reinstalled it, and uninstalled Java 7. I'm using mac 10.9.5, with
> ImageJ version 2.0.0-rc-43/1.50e, build: 49b667f9aa.
>
> It's running with Java 1.6.0_65 [64 bit].
>
> Various scripts that used to work no longer work with this version of Fiji.
> Here's an example:
>
> importClass(Packages.ij.IJ);
> importClass(Packages.ij.plugin.frame.RoiManager);
> importClass(Packages.ij.io.OpenDialog);
> importClass(Packages.ij.io.DirectoryChooser);
> importClass(Packages.java.io.File);
> importClass(Packages.ij.gui.GenericDialog);
> importClass(Packages.ij.util.Tools);
> importClass(Packages.ij.plugin.Duplicator);
> importClass(Packages.ij.measure.ResultsTable);
> importClass(Packages.ij.ImagePlus);
> importClass(Packages.ij.process.ImageProcessor);
> importClass(Packages.ij.util.ArrayUtil);
> importClass(Packages.ij.gui.Overlay);
> importClass(Packages.ij.plugin.filter.ParticleAnalyzer);
> importClass(Packages.ij.gui.Roi);
> importClass(Packages.ij.plugin.RGBStackMerge);
> importClass(Packages.ij.process.ImageConverter);
> importPackage(java.awt);
>
> dir = "/Users/avitalsteinberg/Javascript /RFP wontRun input/";
>
> dirOutput = dir.substring(0, dir.length - 1)+ "_output/";
>
> if(!File(dirOutput).exists()){
> File(dirOutput).mkdir();
> }
>
> IJ = IJ();
> rm = RoiManager(); // initiating the ROI manager in hidden mode.
> if (rm==null)
> IJ.error("ROI Manager is not found");
> rt = ResultsTable(); // Here, the default is hidden mode.
> rt.setValue("yCentroid", 0, 1);
> rt.show();
>
> The debugger gives the following error message: (even though the import
> exits, highlighted blue)
> Can't find method ij.measure.ResultsTable.show()
>
> Any idea what can be done to get Fiji to work well with my computer?
>
> Thanks,
> Avital
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

Avital Steinberg

Re: Problems with Fiji after Fiji update

Hi Brandon,
I have Java 8 installed, but I was unable to get it to work with Fiji. Fiji
still works with Java 6.

How would I get Fiji to work with Java 8?

Thanks,
Avital

On Wed, Dec 2, 2015 at 10:12 PM, Brandon Hurr <[hidden email]>
wrote:

> I don't know for sure, but try running it with Java 8. I have update 51,
> 60, and 66 and they all work fairly well, especially after the 1.50e
> update.
>
> https://www.java.com/en/download/
>
> On Wed, Dec 2, 2015 at 12:07 PM, Avital Steinberg <
> [hidden email]
> > wrote:
>
> > Hi,
> > Ever since I updated Fiji, I'm having trouble using it. I uninstalled it
> > and reinstalled it, and uninstalled Java 7. I'm using mac 10.9.5, with
> > ImageJ version 2.0.0-rc-43/1.50e, build: 49b667f9aa.
> >
> > It's running with Java 1.6.0_65 [64 bit].
> >
> > Various scripts that used to work no longer work with this version of
> Fiji.
> > Here's an example:
> >
> > importClass(Packages.ij.IJ);
> > importClass(Packages.ij.plugin.frame.RoiManager);
> > importClass(Packages.ij.io.OpenDialog);
> > importClass(Packages.ij.io.DirectoryChooser);
> > importClass(Packages.java.io.File);
> > importClass(Packages.ij.gui.GenericDialog);
> > importClass(Packages.ij.util.Tools);
> > importClass(Packages.ij.plugin.Duplicator);
> > importClass(Packages.ij.measure.ResultsTable);
> > importClass(Packages.ij.ImagePlus);
> > importClass(Packages.ij.process.ImageProcessor);
> > importClass(Packages.ij.util.ArrayUtil);
> > importClass(Packages.ij.gui.Overlay);
> > importClass(Packages.ij.plugin.filter.ParticleAnalyzer);
> > importClass(Packages.ij.gui.Roi);
> > importClass(Packages.ij.plugin.RGBStackMerge);
> > importClass(Packages.ij.process.ImageConverter);
> > importPackage(java.awt);
> >
> > dir = "/Users/avitalsteinberg/Javascript /RFP wontRun input/";
> >
> > dirOutput = dir.substring(0, dir.length - 1)+ "_output/";
> >
> > if(!File(dirOutput).exists()){
> > File(dirOutput).mkdir();
> > }
> >
> > IJ = IJ();
> > rm = RoiManager(); // initiating the ROI manager in hidden mode.
> > if (rm==null)
> > IJ.error("ROI Manager is not found");
> > rt = ResultsTable(); // Here, the default is hidden mode.
> > rt.setValue("yCentroid", 0, 1);
> > rt.show();
> >
> > The debugger gives the following error message: (even though the import
> > exits, highlighted blue)
> > Can't find method ij.measure.ResultsTable.show()
> >
> > Any idea what can be done to get Fiji to work well with my computer?
> >
> > Thanks,
> > Avital
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> >
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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ImageJ mailing list: http://imagej.nih.gov/ij/list.html

ctrueden

Re: Problems with Fiji after Fiji update

In reply to this post by Avital Steinberg

Hi Avital,

> The debugger gives the following error message: (even though the
> import exits, highlighted blue) Can't find method
> ij.measure.ResultsTable.show()

I am surprised that your script ever worked, because the ResultsTable class
does not have a show() method (with no arguments).

At first I thought maybe an older version of ImageJ 1.x had one, but I
checked back through ImageJ 1.48p AFAICT there was never a show() method.

There is a show(String) method, so you could try writing:

rt.show("Results");

Regards,
Curtis

On Wed, Dec 2, 2015 at 2:07 PM, Avital Steinberg <[hidden email]>
wrote:

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ImageJ mailing list: http://imagej.nih.gov/ij/list.html

Avital Steinberg

Re: Problems with Fiji after Fiji update

In reply to this post by Avital Steinberg

Actually, I get exactly the same bug when I run ImageJ 1.50e with 1.8.0_66,
so the issue won't be solved by updating Java.

Any idea what can explain this?

Thanks,
Avital

On Wed, Dec 2, 2015 at 10:27 PM, Avital Steinberg <[hidden email]
> wrote:

> Hi Brandon,
> I have Java 8 installed, but I was unable to get it to work with Fiji.
> Fiji still works with Java 6.
>
> How would I get Fiji to work with Java 8?
>
> Thanks,
> Avital
>
> On Wed, Dec 2, 2015 at 10:12 PM, Brandon Hurr <[hidden email]>
> wrote:
>
>> I don't know for sure, but try running it with Java 8. I have update 51,
>> 60, and 66 and they all work fairly well, especially after the 1.50e
>> update.
>>
>> https://www.java.com/en/download/
>>
>> On Wed, Dec 2, 2015 at 12:07 PM, Avital Steinberg <
>> [hidden email]
>> > wrote:
>>
>> > Hi,
>> > Ever since I updated Fiji, I'm having trouble using it. I uninstalled it
>> > and reinstalled it, and uninstalled Java 7. I'm using mac 10.9.5, with
>> > ImageJ version 2.0.0-rc-43/1.50e, build: 49b667f9aa.
>> >
>> > It's running with Java 1.6.0_65 [64 bit].
>> >
>> > Various scripts that used to work no longer work with this version of
>> Fiji.
>> > Here's an example:
>> >
>> > importClass(Packages.ij.IJ);
>> > importClass(Packages.ij.plugin.frame.RoiManager);
>> > importClass(Packages.ij.io.OpenDialog);
>> > importClass(Packages.ij.io.DirectoryChooser);
>> > importClass(Packages.java.io.File);
>> > importClass(Packages.ij.gui.GenericDialog);
>> > importClass(Packages.ij.util.Tools);
>> > importClass(Packages.ij.plugin.Duplicator);
>> > importClass(Packages.ij.measure.ResultsTable);
>> > importClass(Packages.ij.ImagePlus);
>> > importClass(Packages.ij.process.ImageProcessor);
>> > importClass(Packages.ij.util.ArrayUtil);
>> > importClass(Packages.ij.gui.Overlay);
>> > importClass(Packages.ij.plugin.filter.ParticleAnalyzer);
>> > importClass(Packages.ij.gui.Roi);
>> > importClass(Packages.ij.plugin.RGBStackMerge);
>> > importClass(Packages.ij.process.ImageConverter);
>> > importPackage(java.awt);
>> >
>> > dir = "/Users/avitalsteinberg/Javascript /RFP wontRun input/";
>> >
>> > dirOutput = dir.substring(0, dir.length - 1)+ "_output/";
>> >
>> > if(!File(dirOutput).exists()){
>> > File(dirOutput).mkdir();
>> > }
>> >
>> > IJ = IJ();
>> > rm = RoiManager(); // initiating the ROI manager in hidden mode.
>> > if (rm==null)
>> > IJ.error("ROI Manager is not found");
>> > rt = ResultsTable(); // Here, the default is hidden mode.
>> > rt.setValue("yCentroid", 0, 1);
>> > rt.show();
>> >
>> > The debugger gives the following error message: (even though the import
>> > exits, highlighted blue)
>> > Can't find method ij.measure.ResultsTable.show()
>> >
>> > Any idea what can be done to get Fiji to work well with my computer?
>> >
>> > Thanks,
>> > Avital
>> >
>> > --
>> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>> >
>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>
>
>

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ImageJ mailing list: http://imagej.nih.gov/ij/list.html